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Asym./Biol. Unit - manually (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF GALACTOSE MUTAROTASE FROM LACTOCOCCUS LACTIS COMPLEXED WITH L-ARABINOSE

Authors :   J. B. Thoden, J. Kim, R. M. Raushel, H. M. Holden

Date :   04 Sep 02 (Deposition) - 18 Sep 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Epimerase, Sugar Binding, Galactosemia, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Thoden, J. Kim, F. M. Raushel, H. M. Holden
Structural And Kinetic Studies Of Sugar Binding To Galactose Mutarotase From Lactococcus Lactis.
J. Biol. Chem. V. 277 45458 2002
PubMed-ID: 12218067 | Reference-DOI: 10.1074/JBC.M208395200
(for further references see the PDB file header)

Molecule 1 - ALDOSE 1-EPIMERASE
	Chains	:	A, B
	EC Number	:	5.1.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GALM
	Mutation	:	YES
	Organism Scientific	:	LACTOCOCCUS LACTIS
	Organism Taxid	:	1358
	Synonym	:	GALACTOSE MUTAROTASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	ARB	2	Ligand/Ion	BETA-L-ARABINOSE
2	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:71 , HIS A:96 , HIS A:170 , ASP A:243 , PHE A:279 , GLU A:304 , HOH A:441	BINDING SITE FOR RESIDUE ARB A 348
2	AC2	SOFTWARE	ARG B:71 , HIS B:96 , HIS B:170 , GLU B:203 , ASP B:243 , PHE B:279 , GLU B:304 , HOH B:392 , HOH B:510	BINDING SITE FOR RESIDUE ARB B 348
3	AC3	SOFTWARE	ASP A:13 , HOH A:354 , ASP B:13 , HIS B:346 , HOH B:367	BINDING SITE FOR RESIDUE NA A 349

(no "SS Bond" information available for 1MMZ)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:66	-	Pro A:67
2	Gly A:135	-	Lys A:136
3	Gly B:66	-	Pro B:67
4	Gly B:135	-	Lys B:136

(no "SAP(SNP)/Variant" information available for 1MMZ)

(no "PROSITE Motif" information available for 1MMZ)

(no "Exon" information available for 1MMZ)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:339
 aligned with Q9ZB17_9LACT | Q9ZB17 from UniProtKB/TrEMBL  Length:339

    Alignment length:339
                                                                                                                                                                                                                                                                                                                                                                           339 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       | 
         Q9ZB17_9LACT     2 EIKIRDFGLGSDLISLTNKAGVTISFTNLGARIVDWQKDGKHLILGFDSAKEYLEKDAYPGATVGPTAGRIKDGLVKISGKDYILNQNEGPQTLHGGEESIHTKLWTYEVTDLGAEVQVKFSLVTNDGTNGYPGKIEMSVTHSFDDYNKWKIHYEAISDKDTVFNPTGHVYFNLNGDASESVENHGLRLAASRFVPLKDQTEIVRGDIVDIKNTDLDFRQEKQLSNAFNSNMEQVQLVKGIDHPFLLDQLGLDKEQARLTLDDTSISVFTDQPSIVIFTANFGDLGTLYHEKKQVHHGGITFECQVSPGSEQIPELGDISLKAGEKYQATTIYSLHTK-   -
               SCOP domains d1mmza_ A: Galactose mutarotase                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1mmzA00 A:2-340  [code=2.70.98.10, no name defined]                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee.....eeeee....eeeeeee..ee......hhhhhhhh......ee.....ee...eeee..eeee........ee.....hhhhh..eeeeee...eeeeeeeeee..hhhhh...eeeeeeeeee...eeeeeeeeee...ee...ee..ee........hhhh.eeee.eeee..............ee...........eehhhhhh..hhhhhhhh..eeeeee.........eeeee..eeeeeee...eeeee.........ee..ee......ee.eee.......hhhhh..ee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mmz A   2 SIKIRDFGLGSDLISLTNKAGVTISFTNLGARIVDWQKDGKHLILGFDSAKEYLEKDAYPGATVGPTAGRIKDGLVKISGKDYILNQNEGPQTLHGGEESIHTKLWTYEVTDLGAEVQVKFSLVSNDGTNGYPGKIEMSVTHSFDDDNKWKIHYEAISDKDTVFNPTGHVYFNLNGDASESVENHGLRLAASRFVPLKDQTEIVRGDIVDIKNTDLDFRQEKQLSNAFNSNMEQVQLVKGIDHPFLLDQLGLDKEQARLTLDDTSISVFTDQPSIVIFTANFGDLGTLYHEKKQVHHGGITFECQVSPGSEQIPELGDISLKAGEKYQATTIYSLHTKL 340
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331

Chain B from PDB  Type:PROTEIN  Length:346
 aligned with Q9ZB17_9LACT | Q9ZB17 from UniProtKB/TrEMBL  Length:339

    Alignment length:346
                                                                                                                                                                                                                                                                                                                                                                           339        
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       | -      
         Q9ZB17_9LACT     2 EIKIRDFGLGSDLISLTNKAGVTISFTNLGARIVDWQKDGKHLILGFDSAKEYLEKDAYPGATVGPTAGRIKDGLVKISGKDYILNQNEGPQTLHGGEESIHTKLWTYEVTDLGAEVQVKFSLVTNDGTNGYPGKIEMSVTHSFDDYNKWKIHYEAISDKDTVFNPTGHVYFNLNGDASESVENHGLRLAASRFVPLKDQTEIVRGDIVDIKNTDLDFRQEKQLSNAFNSNMEQVQLVKGIDHPFLLDQLGLDKEQARLTLDDTSISVFTDQPSIVIFTANFGDLGTLYHEKKQVHHGGITFECQVSPGSEQIPELGDISLKAGEKYQATTIYSLHTK--------   -
               SCOP domains d1mmzb_ B: Galactose mutarotase                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1mmzB00 B:2-347  [code=2.70.98.10, no name defined]                                                                                                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) -----------Aldose_epim-1mmzB01 B:13-335                                                                                                                                                                                                                                                                                                       ------------ Pfam domains (1)
           Pfam domains (2) -----------Aldose_epim-1mmzB02 B:13-335                                                                                                                                                                                                                                                                                                       ------------ Pfam domains (2)
         Sec.struct. author .eeeeeee..eeeeeee.....eeeee....eeeeeee..ee......hhhhhhhh......ee.....ee...eeee..eeee........ee.....hhhhh..eeeeee...eeeeeeeeee..hhhhh...eeeeeeeeee...eeeeeeeeee...ee...ee..ee........hhhh.eeee.eeee..............ee...........eehhhhhh..hhhhhhhh..eeeeee.........eeeee..eeeeeee...eeeee.........ee..ee......ee.eee.......hhhhh..ee.....eeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mmz B   2 SIKIRDFGLGSDLISLTNKAGVTISFTNLGARIVDWQKDGKHLILGFDSAKEYLEKDAYPGATVGPTAGRIKDGLVKISGKDYILNQNEGPQTLHGGEESIHTKLWTYEVTDLGAEVQVKFSLVSNDGTNGYPGKIEMSVTHSFDDDNKWKIHYEAISDKDTVFNPTGHVYFNLNGDASESVENHGLRLAASRFVPLKDQTEIVRGDIVDIKNTDLDFRQEKQLSNAFNSNMEQVQLVKGIDHPFLLDQLGLDKEQARLTLDDTSISVFTDQPSIVIFTANFGDLGTLYHEKKQVHHGGITFECQVSPGSEQIPELGDISLKAGEKYQATTIYSLHTKLEHHHHHH 347
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Supersandwich (271)

Superfamily: Galactose mutarotase-like (205)

Family: Aldose 1-epimerase (mutarotase) (23)

Protein domain: Galactose mutarotase (22)

Lactococcus lactis [TaxId: 1358] (19)

1a	d1mmza_	A:
1b	d1mmzb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Distorted Sandwich (506)

Topology: Beta-galactosidase; Chain A, domain 5 (250)

Homologous Superfamily: [code=2.70.98.10, no name defined] (116)

Lactococcus lactis. Organism_taxid: 1358. (7)

1a	1mmzA00	A:2-340
1b	1mmzB00	B:2-347

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Gal_mutarotase (81)

Family: Aldose_epim (24)

Lactococcus lactis (17)

1a	Aldose_epim-1mmzB01	B:13-335
1b	Aldose_epim-1mmzB02	B:13-335

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q9ZB17_9LACT | Q9ZB17)

molecular function
	GO:0004034	aldose 1-epimerase activity	Catalysis of the reaction: alpha-D-glucose = beta-D-glucose. Also acts on L-arabinose, D-xylose, D-galactose, maltose and lactose.
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0006012	galactose metabolic process	The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.
	GO:0019318	hexose metabolic process	The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:135 - Lys A:136	[ RasMol ]
		Gly A:66 - Pro A:67	[ RasMol ]
		Gly B:135 - Lys B:136	[ RasMol ]
		Gly B:66 - Pro B:67	[ RasMol ]

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1mmu	SAME PROTEIN CRYSTALLIZED WITH ALPHA-D-GLUCOSE
1mmx	SAME PROTEIN CRYSTALLIZED WITH FUCOSE
1mmy	SAME PROTEIN CRYSTALLIZED WITH 6-DEOXY-ALPHA-D-GLUCOSE
1mn0	SAME PROTEIN CRYSTALLIZED WITH L-ARABINOSE

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

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Cis Peptide Bonds (4, 4)

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